Table 1.
Data set (coverage) | NGSEP |
CNVNator |
BreakDancer |
GATKb |
SNVer |
SAMtools |
VarScan 2 |
|||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
RTa | RAMa | RT | RAM | RT | RAM | RT | RAM | RT | RAM | RT | RAM | RT | RAM | |
Yeast parent CBS6412 (79×) | 27 min | 1.9 Gb | 1 min | 1.6 Gb | 1 min | 10 Mb | 1 h 41 min | 4.0 Gb | 11 min | 2.6 Gb | 14 min | 40 Mb | 38 min | 5.8 Gb |
Yeast parent ER7A (96×) | 30 min | 2 Gb | 1 min | 1.6 Gb | 1 min | 10 Mb | 1 h 58 min | 4.1 Gb | 14 min | 2.7 Gb | 17 min | 40 Mb | 36 min | 5.8 Gb |
Yeast pool (34×) | 21 min | 1.6 Gb | 1 min | 1.6 Gb | 1 min | 15 Mb | 1 h 35 min | 3.4 Gb | 7 min | 2.7 Gb | 6 min | 35 Mb | 26 min | 5.8 Gb |
Rice IR8 (26×) | 2 h 38 min | 3 Gb | 25 min | 2.3 Gb | 2 h 23 min | 2.8 Gb | 11 h 21 min | 5.8 Gb | – | – | 2 h 43 min | 100 Mb | – | – |
Human chr1 (64×) | 1 h 44 min | 2.7 Gb | 19 min | 2.1 Gb | 15 min | 400 Mb | 1 h 37 min | 200 Mb | 1 h 51 min | 2.8 Gb | 1 h 28 min | 300 Mb | – | – |
Human (5×) | 9 h 25 min | 7.5 Gb | 3 h 46 min | 7.4 Gb | 24 min | 500 Mb | 8 h 20 min | 600 Mb | – | – | 5 h 23 min | 300 Mb | – | – |
a RT: runtime; RAM: random access memory.
b The GATK pipeline was executed as suggested in (9) for the yeast and rice samples. For the human samples only the Unified Genotyper was executed.